I am trying to refine a protein structure where some of the side
chains have 2 possbile configurations, ie. I would like to refine
the occupanices of these 2 possible positions. Does anyone have any
suggestions on this? So far, I have tried building in the 2nd position
of a residue, then refining the occupancies. This seems to work, but when
I try to do any kind of further positional refinement of the protien, there
are too many bad contacts and it dies. There are bad contacts because the 2nd
position of the residue is obviously close to the first, etc. I don't
see any way around this. Any help would be appreciated
Matt Pugmire
pugmire at bio.cornell.edu